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- PDB-4jbn: Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba... -

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Basic information

Entry
Database: PDB / ID: 4jbn
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba histolytica in complex with Serine acetyl transferase derived tetrapeptide, SPSI
Components
  • Cysteine synthase
  • SAT derived tetrapeptide
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Cysteine Synthase / peptide inhibitor / PLP fold type 2 / Tryptophan synthase family / lyase / Serine Acetyl Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


cysteine synthase activity / L-cysteine biosynthetic process from L-serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies
Authors: Raj, I. / Mazumder, M. / Gourinath, S.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
C: SAT derived tetrapeptide
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7724
Polymers74,6763
Non-polymers961
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-51 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.515, 80.515, 112.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cysteine synthase / O-Acetyl Serine Sulfhydrylase


Mass: 37136.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhOASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15570
#2: Protein/peptide SAT derived tetrapeptide


Mass: 402.443 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2.1M AmSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 30, 2008
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→27.47 Å / Num. all: 58947 / Num. obs: 58645 / % possible obs: 94.6 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 3.6
Reflection shellResolution: 1.868→1.917 Å / % possible all: 90.77

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
AUTOMARdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQM

2pqm


Resolution: 1.87→27.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.747 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 2873 4.9 %RANDOM
Rwork0.1843 ---
all0.2398 ---
obs0.1861 58645 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.2 Å2 / Biso mean: 27.6853 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 5 251 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195254
X-RAY DIFFRACTIONr_angle_refined_deg2.131.9847090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94625.419203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24315960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.591520
X-RAY DIFFRACTIONr_chiral_restr0.1560.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213846
LS refinement shellResolution: 1.868→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 177 -
Rwork0.277 3788 -
all-3965 -
obs--90.77 %

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